HEADER APOPTOSIS, TRANSPORT PROTEIN 03-APR-13 4JZL TITLE CRYSTAL STRUCTURE OF BAP31 VDED AT ALKALINE PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-CELL RECEPTOR-ASSOCIATED PROTEIN 31; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: VDED DOMAIN: UNP RESIDUES 168-223; COMPND 5 SYNONYM: BCR-ASSOCIATED PROTEIN 31, BAP31, 6C6-AG TUMOR-ASSOCIATED COMPND 6 ANTIGEN, PROTEIN CDM, P28; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BCAP31, BAP31, DXS1357E; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSETTA 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS APOPTOSIS, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.M.QUISTGAARD,C.LOW,P.MOBERG,F.GUETTOU,K.MADDI,P.NORDLUND REVDAT 2 20-SEP-23 4JZL 1 REMARK SEQADV REVDAT 1 25-SEP-13 4JZL 0 JRNL AUTH E.M.QUISTGAARD,C.LOW,P.MOBERG,F.GUETTOU,K.MADDI,P.NORDLUND JRNL TITL STRUCTURAL AND BIOPHYSICAL CHARACTERIZATION OF THE JRNL TITL 2 CYTOPLASMIC DOMAINS OF HUMAN BAP29 AND BAP31. JRNL REF PLOS ONE V. 8 71111 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23967155 JRNL DOI 10.1371/JOURNAL.PONE.0071111 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 13771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.030 REMARK 3 FREE R VALUE TEST SET COUNT : 555 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.3429 - 3.4905 0.98 3376 118 0.2040 0.2199 REMARK 3 2 3.4905 - 2.7712 0.99 3344 133 0.2224 0.2373 REMARK 3 3 2.7712 - 2.4211 0.99 3253 155 0.2404 0.2867 REMARK 3 4 2.4211 - 2.1999 0.98 3243 149 0.2576 0.2987 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 2013 REMARK 3 ANGLE : 0.680 2671 REMARK 3 CHIRALITY : 0.048 302 REMARK 3 PLANARITY : 0.002 348 REMARK 3 DIHEDRAL : 15.404 842 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' OR CHAIN 'D') REMARK 3 ORIGIN FOR THE GROUP (A): 35.7196 9.8792 3.2161 REMARK 3 T TENSOR REMARK 3 T11: 0.1395 T22: 0.2589 REMARK 3 T33: 0.1609 T12: 0.0072 REMARK 3 T13: -0.0271 T23: 0.0342 REMARK 3 L TENSOR REMARK 3 L11: 0.2856 L22: 0.3356 REMARK 3 L33: -0.0446 L12: -0.0743 REMARK 3 L13: -0.0383 L23: 0.2880 REMARK 3 S TENSOR REMARK 3 S11: 0.0196 S12: 0.1792 S13: 0.0803 REMARK 3 S21: -0.0442 S22: 0.0159 S23: -0.0142 REMARK 3 S31: -0.0072 S32: -0.3816 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' OR CHAIN 'C') REMARK 3 ORIGIN FOR THE GROUP (A): 48.7881 10.2299 26.7316 REMARK 3 T TENSOR REMARK 3 T11: 0.1950 T22: 0.1455 REMARK 3 T33: 0.1930 T12: 0.0036 REMARK 3 T13: 0.0016 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.1982 L22: 0.0019 REMARK 3 L33: 0.1393 L12: 0.1415 REMARK 3 L13: 0.0782 L23: -0.2008 REMARK 3 S TENSOR REMARK 3 S11: 0.0433 S12: -0.0578 S13: 0.0119 REMARK 3 S21: 0.0253 S22: 0.0126 S23: 0.0278 REMARK 3 S31: -0.0368 S32: 0.2099 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JZL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13838 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 28.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.57500 REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4JZP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, 34% PEG2000 REMARK 280 MONOMETHYL ETHER (MME) AND 150 MM KBR, PH 8.0, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 21.45000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 166 REMARK 465 MET A 167 REMARK 465 LEU A 168 REMARK 465 ASP A 169 REMARK 465 VAL A 170 REMARK 465 GLY A 171 REMARK 465 SER B 166 REMARK 465 MET B 167 REMARK 465 LEU B 168 REMARK 465 ASP B 169 REMARK 465 VAL B 170 REMARK 465 GLY B 171 REMARK 465 ASN B 172 REMARK 465 SER C 166 REMARK 465 MET C 167 REMARK 465 LEU C 168 REMARK 465 ASP C 169 REMARK 465 VAL C 170 REMARK 465 GLY C 171 REMARK 465 SER D 166 REMARK 465 MET D 167 REMARK 465 LEU D 168 REMARK 465 ASP D 169 REMARK 465 VAL D 170 REMARK 465 GLY D 171 REMARK 465 ASN D 172 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JZP RELATED DB: PDB DBREF 4JZL A 168 233 UNP P51572 BAP31_HUMAN 168 233 DBREF 4JZL B 168 233 UNP P51572 BAP31_HUMAN 168 233 DBREF 4JZL C 168 233 UNP P51572 BAP31_HUMAN 168 233 DBREF 4JZL D 168 233 UNP P51572 BAP31_HUMAN 168 233 SEQADV 4JZL SER A 166 UNP P51572 EXPRESSION TAG SEQADV 4JZL MET A 167 UNP P51572 EXPRESSION TAG SEQADV 4JZL SER B 166 UNP P51572 EXPRESSION TAG SEQADV 4JZL MET B 167 UNP P51572 EXPRESSION TAG SEQADV 4JZL SER C 166 UNP P51572 EXPRESSION TAG SEQADV 4JZL MET C 167 UNP P51572 EXPRESSION TAG SEQADV 4JZL SER D 166 UNP P51572 EXPRESSION TAG SEQADV 4JZL MET D 167 UNP P51572 EXPRESSION TAG SEQRES 1 A 68 SER MET LEU ASP VAL GLY ASN ALA GLU VAL LYS LEU GLU SEQRES 2 A 68 GLU GLU ASN ARG SER LEU LYS ALA ASP LEU GLN LYS LEU SEQRES 3 A 68 LYS ASP GLU LEU ALA SER THR LYS GLN LYS LEU GLU LYS SEQRES 4 A 68 ALA GLU ASN GLN VAL LEU ALA MET ARG LYS GLN SER GLU SEQRES 5 A 68 GLY LEU THR LYS GLU TYR ASP ARG LEU LEU GLU GLU HIS SEQRES 6 A 68 ALA LYS LEU SEQRES 1 B 68 SER MET LEU ASP VAL GLY ASN ALA GLU VAL LYS LEU GLU SEQRES 2 B 68 GLU GLU ASN ARG SER LEU LYS ALA ASP LEU GLN LYS LEU SEQRES 3 B 68 LYS ASP GLU LEU ALA SER THR LYS GLN LYS LEU GLU LYS SEQRES 4 B 68 ALA GLU ASN GLN VAL LEU ALA MET ARG LYS GLN SER GLU SEQRES 5 B 68 GLY LEU THR LYS GLU TYR ASP ARG LEU LEU GLU GLU HIS SEQRES 6 B 68 ALA LYS LEU SEQRES 1 C 68 SER MET LEU ASP VAL GLY ASN ALA GLU VAL LYS LEU GLU SEQRES 2 C 68 GLU GLU ASN ARG SER LEU LYS ALA ASP LEU GLN LYS LEU SEQRES 3 C 68 LYS ASP GLU LEU ALA SER THR LYS GLN LYS LEU GLU LYS SEQRES 4 C 68 ALA GLU ASN GLN VAL LEU ALA MET ARG LYS GLN SER GLU SEQRES 5 C 68 GLY LEU THR LYS GLU TYR ASP ARG LEU LEU GLU GLU HIS SEQRES 6 C 68 ALA LYS LEU SEQRES 1 D 68 SER MET LEU ASP VAL GLY ASN ALA GLU VAL LYS LEU GLU SEQRES 2 D 68 GLU GLU ASN ARG SER LEU LYS ALA ASP LEU GLN LYS LEU SEQRES 3 D 68 LYS ASP GLU LEU ALA SER THR LYS GLN LYS LEU GLU LYS SEQRES 4 D 68 ALA GLU ASN GLN VAL LEU ALA MET ARG LYS GLN SER GLU SEQRES 5 D 68 GLY LEU THR LYS GLU TYR ASP ARG LEU LEU GLU GLU HIS SEQRES 6 D 68 ALA LYS LEU HET GOL A 301 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *114(H2 O) HELIX 1 1 ASN A 172 LYS A 232 1 61 HELIX 2 2 GLU B 174 ALA B 231 1 58 HELIX 3 3 ALA C 173 LEU C 233 1 61 HELIX 4 4 GLU D 174 ALA D 231 1 58 SITE 1 AC1 3 GLU A 229 LYS A 232 LYS C 214 CRYST1 56.690 42.900 62.670 90.00 115.87 90.00 P 1 21 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017640 0.000000 0.008553 0.00000 SCALE2 0.000000 0.023310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017733 0.00000